Glad to see your training has intensified mate, last time you discussed it you weren't doing a lot oweing to your knee issues, does this mean you're free of ITBS?
At the risk of being told to STFU i'd probably say from my own experiences that you're addressing a problem that doesn't exist. My first ever fellrace was an AM and i never dropped to shorts until i had my knee issues started, once my quads were over the shock of the increase in exertion it was plain sailing. The only thing seems to be that mediums tend to have more flattish bits compared to shorts so any improvement in your stamina will help to stop you using these sections as rests.
My opinion would be that it's more of a mental battle really, on the Dufton Pike race that 2m flat section before and after the Pike is a real tw@t if you're gunning it, maintaining your max speed becomes a real fight and the Settle Tough Trail is just 10m of that all the way round.
Got out on my push iron for a cheeky 20 miler last night, i gave it up when my knee started but i'm going to have to crack on with it to keep my aerobic fitness up. I used to swim a lot too but i can't do with the crowds and the grannies in the fast lane going to get back into it as i plan to do a Tri this year and need to learn to swim F/C without drowning.